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The tunnel under New York City's East River that carries the R subway train will be closed for more than a year to repair damage caused by Hurricane Sandy, the Metropolitan Transportation Authority announced today.

About 65,000 riders use the R train every weekday.

Those traveling to Manhattan can transfer to one of 11 lines that are accessible from four R stations in Brooklyn.

R train service between Brooklyn and Manhattan was restored a few weeks after Sandy hit, thanks to short-term repairs.

But the Montague tube had been filled with 27 million gallons of salt water for ten days before it was pumped out, causing serious damage to electrical components, cables, and walkways.

The long-term fix will take 14 months and start in August. The MTA estimates it will cost at least $100 million.

Making repairs in a subway system that operates 24 hours a day is difficult, and if the MTA worked on the tunnel only on nights and weekends, the project would run into 2016, it said.

The MTA also announced it will close the Greenpoint Tube, which carries the G train between Brooklyn and Queens, for 12 weekends starting July 6.

The MTA noted "this will be a fast-tracked solicitation in order to make an award as soon as possible."

The R train runs from Forest Hills in Queens, along Broadway in Manhattan, and under the East River into Brooklyn. It ends in Bay Ridge, near the foot of the Verrazano-Narrows Bridge.

The usually cash-strapped MTA actually has a $40 million surplus, thanks to state aid. In a letter addressed to MTA Acting Chairman Fernando Ferrer, eight candidates for NYC mayor called on the Authority to use the money to "maintain and increase service," but made no mention of repairs in the wake of Sandy.

An MTA spokesperson clarified that the governor's budget allocated the Authority at least $25 million more than it anticipated, and that the number could rise by $15 million if "certain tax revenues perform very well." The MTA will present on its financial situation to its board in July.